Mono- and bichromatic electron dynamics: LiH, a test case

This paper describes an electron dynamics method where the time dependence of an external oscillating electric field is the perturbing part of the Hamiltonian. Application of the electric field induces charge movement inside the molecule and electronic transitions between the molecular orbitals. The test system is the neutral LiH molecule. The method is applied to wave functions calculated using the B3LYP (hybrid) density functional, with the STO-3G and the 6-31+G basis sets. The molecule undergoes full population inversion between the HOMO and the LUMO when the electric field is in resonance with the HOMO-LUMO energy gap. The magnitude of the electric field directly affects the rate at which electronic transitions occur and the rate at which charges move between lithium and hydrogen atoms. The method is used to model both monochromatic and bichromatic multiphoton effects in LiH. Monochromatic one-, two- and three-photon transitions occur between the HOMO, LUMO and two other virtual orbitals. There is evidence of both [1+2] direct and [1+1+1] stepwise multiphoton transitions. Bichromatically, two "laser" pulses are applied at different frequencies. Electronic transitions can be fine-tuned to occur via pre-specified pathways of virtual molecular orbitals.     

Inelastic electron tunneling spectroscopy in molecular junctions: peaks and dips

We study inelastic electron tunneling through a molecular junction using the nonequilibrium Green's function formalism. The effect of the mutual influence between the phonon and the electron subsystems on the electron tunneling process is considered within a general self-consistent scheme. Results of this calculation are compared to those obtained from the simpler Born approximation and the simplest perturbation theory approaches, and some shortcomings of the latter are pointed out. The self-consistent calculation allows also for evaluating other related quantities such as the power loss during electron conduction. Regarding the inelastic spectrum, two types of inelastic contributions are discussed. Features associated with real and virtual energy transfer to phonons are usually observed in the second derivative of the current I with respect to the voltage Phi when plotted against Phi. Signatures of resonant tunneling driven by an intermediate molecular ion appear as peaks in the first derivative dI/dPhi and may show phonon sidebands. The dependence of the observed vibrationally induced lineshapes on the junction characteristics, and the linewidth associated with these features are also discussed.     

Graph theory of synthons

A graph-theory model of synthons is suggested. A synthon is a special kind of the molecular graph in which some vertices are distinguished from other ones, and they are called the virtual vertices. The most important property of the synthons is that the constraint of strict stoichiometry is removed and the virtual vertices formally correspond to functional groups that are not closely specified.     

Configurational statistics of polynucleotide chains. A single virtual bond treatment.

A simplified single virtual bond scheme has been developed for the calculation of mean-square unperturbed dimensions in polynucleotide chains. As a consequence of the structural rigidity of the sugar residues in the chain, it is possible to represent the six chemical bonds comprising the chain backbone repeating unit by a single virtual bond (connecting successive phosphorus atoms). The mutual orientation of a pair of adjoining virtual bonds is determined by the angles of rotation about the phosphodiester bonds adjoining intervening phosphorus atoms and is independent of the orientation of all other virtual bonds in the chain. Computed values of chain dimensions based on the single virtual bond scheme are comparable to those calculated previously using a two virtual bond model which permits rotational flexibility in the sugar moieties of the chain.     

Analyzing the electric response of molecular conductors using “electron deformation” orbitals and occupied‐virtual electron transfer

The concept of “electron deformation orbitals” (EDOs) is used to investigate the electric response of conducting metals and oligophenyl chains. These orbitals and their eigenvalues are obtained by diagonalization of the deformation density matrix (difference between the density matrices of the perturbed and unperturbed systems) and can be constructed as linear combinations of the unperturbed molecular orbitals within “frozen geometry” conditions. This form of the EDOs allows calculating the part of the electron deformation density associated to an effective electron transfer from occupied to virtual orbitals (valence to conduction band electron transfer in the band model of conductivity). It is found that the “electron deformation” orbitals pair off, displaying the same eigenvalue but opposite sign. Each pair represents an amount of accumulation/depletion of electron charge at different molecular regions. In the oligophenyl systems investigated only one pair contributes effectively to the charge flow between molecular ends, resulting from the promotion of electrons from occupied orbitals to close in energy virtual orbitals of appropriate symmetry and overlapping. Analysis of this pair along explains the differences in conductance of olygophenyl chains based on phenyl units. © 2014 Wiley Periodicals, Inc.     

Pharmacophore identification, in silico screening, and virtual library design for inhibitors of the human factor Xa

Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entries 1fjs, 1kns, 1eqz) using the software LIGANDSCOUT and CATALYST. The complex structures were selected regarding the criteria of high inhibitory potency (i.e. all ligands show K(i) values against factor Xa in the subnanomolar range) and good resolution (i.e. at least 2.2 A) in order to generate selective and high quality pharmacophore models. The resulting chemical-feature based hypotheses were used for virtual screening of commercial molecular databases such as the WDI database. Furthermore, a ligand-based molecular modeling approach was performed to obtain common-feature hypotheses that represent the relevant chemical interactions between 10 bioactive factor Xa inhibitors and the protein, respectively. In a next step a virtual combinatorial library was designed in order to generate new compounds with similar chemical and spatial properties as known inhibitors. The software tool ILIB DIVERSE was used for this procedure in order to provide new scaffolds of this group of anticoagulants. Finally we present the combination of these two techniques, hence virtual screening was performed with selective pharmacophore models in a focused virtual combinatorial database. De novo derived molecular scaffolds that were able to adequately satisfy the pharmacophore criteria are revealed and are promising templates for candidates for further development.     

A self-consistent coulomb bath model using density fitting

A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Importantly, the present Coulomb bath is represented using a density fitting method in which the electron densities of molecular fragments are fitted using an atom-centered auxiliary basis set of Gaussian type. The Coulomb bath is incorporated into an effective Hamiltonian for each fragment, with which the electron density is optimized through an iterative double self-consistent field (DSCF) procedure to realize the mutual many-body polarization effects. In this work, the accuracy of interfragment interaction energies enumerated using the Coulomb bath is tested, showing a good agreement with the exact results from an energy decomposition analysis. The qualitative features of many-body polarization effects are visualized by electron density difference plots. It is also shown that the present DSCF method can yield fast and robust convergence with near-linear scaling in performance with increase in system size.     

Gating of single molecule transistors: combining field-effect and chemical control

Previously we have demonstrated that several structural features are crucial for the functionality of molecular field-effect transistors. The effect of additional structural aspects of molecular wires is explored. These include the type of, the thiol binding location on, and the chemical substitutions of a conjugated system. Pentacene, porphyrin, and the Tour-Reed devices are utilized as model systems. The thiol binding location is shown to have a varied effect on the transmission of a system depending on the molecular orbitals involved. Substitution by electron withdrawing and donating groups is illustrated to have a substantial effect on the transmission of single molecule devices. The substitution effect is either a simple energy shifting effect or a more complicated resonance effect, and can be used to effectively tune the electronic behavior of a single molecule field effect transistor.     

论络合物中心过渡金属离子的径向波函数

考虑中心对称配体场影响,提出一种不同基混合的束缚态过渡金属离子的3d径向波函数。利用这种波函数,计算了一些Cu⁺⁺络离子的晶场谱。假设适当的边界条件,用一个拟合参数,就能得到和实验一致的结果。这种方法的实质在于,在晶体场静止点荷模型基础上,考虑了诸配体等效中心对称场的部份分子轨道效应。这种混合基单电子3d径向波函数也能用于完全的分子轨道理论计算。     

Reassessment of large dipole moment enhancements in crystals: a detailed experimental and theoretical charge density analysis of 2-methyl-4-nitroaniline

The molecular dipole moment of MNA in the crystal has been critically reexamined, to test the conclusion from an earlier experimental charge density analysis that it was substantially enhanced due to a combination of strong intermolecular interactions and crystal field effects. X-ray and neutron diffraction data have been carefully measured at 100 K and supplemented with ab initio crystal Hartree-Fock calculations. Considerable care taken in the measurement and reduction of the experimental data excluded most systematic errors, and sources of error and their effects on the experimental electron density have been carefully investigated. The electron density derived from a fit to theoretical structure factors assisted in the determination of the scale and thermal motion model. The dipole moment enhancement for MNA in the crystal is much less than that reported previously and only on the order of 30-40% (approximately 2.5 D). In addition to the dipole moment, experimental deformation electron density maps, bond critical point data, electric field gradients at hydrogen nuclei, and atomic and group charges all agree well with theoretical results and trends. Anisotropic modeling of the motion of hydrogen atoms, integral use of periodic ab initio calculations, and improved data quality are all aspects of this study that represent a considerable advance over previous work.     

Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals

Extremely localized molecular orbitals (ELMOs), namely orbitals strictly localized on molecular fragments, are easily transferable from one molecule to another one. Hence, they provide a natural way to set up the electronic structure of large molecules using a data base of orbitals obtained from model molecules. However, this procedure obviously increases the energy with respect to a traditional MO calculation. To gain accuracy, it is important to introduce a partial electron delocalization. This can be carried out by defining proper optimal virtual orbitals that supply an efficient set for nonorthogonal configurations to be employed in VB-like expansions.     

Magnetic field effects on exciplex-forming systems: the effect on the locally excited fluorophore and its dependence on free energy

This study addresses magnetic field effects in exciplex forming donor-acceptor systems. For moderately exergonic systems, the exciplex and the locally excited fluorophore emission are found to be magneto-sensitive. A previously introduced model attributing this finding to excited state reversibility is confirmed. Systems characterised by a free energy of charge separation up to approximately -0.35 eV are found to exhibit a magnetic field effect on the fluorophore. A simple three-state model of the exciplex is introduced, which uses the reaction distance and the asymmetric electron transfer reaction coordinate as pertinent variables. Comparing the experimental emission band shapes with those predicted by the model, a semi-quantitative picture of the formation of the magnetic field effect is developed based on energy hypersurfaces. The model can also be applied to estimate the indirect contribution of the exchange interaction, even if the perturbative approach fails. The energetic parameters that are essential for the formation of large magnetic field effects on the exciplex are discussed.